Allison killed Francie inside of her restaurant, shooting her in the forehead whilst she was talking to her mother on the phone. After killing her, Allison received a call from Julian Sark. She then said that "Everything's in place." (Phase One).

From there on, Allison posed as Francie Calfo while simultaneously taking orders from Sloane and Sark. Despite everything, she never raised any suspicion. However, when Sydney and Allison were at a cafe, Francie presented a gift to give to Michael even though she barely knew him. Sydney was wondering how Francie knew what kind of suit Vaughn would wear, but Allison managed to lie her way out of the accusation.

Her life with Sloane and Sark didn't cease, as she was ordered to perform a few tasks for the two of them. At one point she executed a plumber to frame him for planting the bugs found in Sydneys home. The second task was more serious however. After Dixon accidentally killed Sloane's wife during a raid on his villa, he ordered Allison to kill Dixon's wife, Diane, which she did via a car bomb.

Allison was finally ordered to blow her cover and kill both Will and Sydney. Allison pinned Will onto the wall of the house and stabbed him in the chest, crying as she did so. She hid the body in the bathtub and waited for Sydney to come back home (The Telling).

When she did, Sydney was getting more and more suspicious of "Francie" because Will wasn't home and she was too calm. Sydney offered her coffee ice cream (which she accepted) and then ran into her room to get her gun. Allison showed up and said, "I just remembered...Francie doesn't like coffee ice cream." realizing she blew her cover. The two engaged in a fierce fist fight around the house, using everything they could find in order to subdue the other combatant. During the fight, Sydney found Will's body lying in the bathtub, thinking she had already killed him (The Telling).

The fight reached its climax when Allison slammed Sydney into a mirror (possibly piercing her spine with a shard of glass) and Sydney fell to the floor, unable to fight any longer. Allison slowly reached for Sydney's gun, but Sydney slit her face with a large piece of glass and got the gun herself. She aimed the gun at Allison and shot her in the arm and chest twice, supposedly killing her (The Telling).

Allison was seen once again returning to Julian Sark after supposedly dying the previous two years. While in bed, Allison explained how she survived the gunshot wounds and how a medication from a Rambaldi journal healed her wounds.

Allison was ordered by Sark to locate a device that acted as a launch control for a nuclear arsenal in a nightclub, which was guarded by two men: Heinrich Strauss and Robert Lange. Allison killed Heinrich with a sniper and after encountering resistance from Michael and Sydney, she eventually found Lange and extracted his tooth shortly before killing him. Sydney finds the body and is knocked out by Allison, but not killed.

While meeting with Sloane in Prague (who was a double agent at the time) Allison told him that the only reason why she didn't kill Sydney was because there was something in her brain The Covenant needed. Afterwards, Sark reveals where the location of the device is.

Sydney encounters Allison again in Sofia and she explains how she was able to survive for so long. Just as Allison is about to kill Sydney, Sydney knocks the gun out her hand and they get into a fight again, which results in Allison getting shot. However, as she is hoisted away to the hospital, she kills all the paramedics and escapes, despite barely having a pulse. (The Nemesis)

Allison, shortly after she's stabbed by Will.

While accompanying Sark on a mission to retrieve a safe deposit box belonging to Julia Thorne, she encounters Tippin and the two engage in a fight while Sydney chases after Sark. During the fight, Allison pulls out a knife and tries to slash Will with it. After hitting her in the head with a light fixture, he grabs her hands and pins her to the wall with the knife aimed at her chest. Will angrily mutters, "This is for Francie." and plunges the knife into her chest, simila